A Fresh Start
by Miranda Herondale
Summary: Sequel to Isabelle Lightwood, Maybe. If you haven't read it, do! How do the lives of our favorite characters change with Isabelle and Clary's news? Will there be Clace babies? Or does something happen to Clary? There will be a new occupant of the New York institute as well. Who might this be? And when bad sorts of people find out, what will they want? Read and discover!
1. Prologue

**Hey! So this is my sequel to **_**Isabelle Lightwood, Maybe. **_**If you haven't read it, i suggest you do, or you shall be confused. I hope it is good. As I go along, Give me ideas. I love hearing them. If you think I can improve on something, let me know. Constructive Criticism is very welcome! As are questions. Talk to me! Here is your Prologue. **

**Prologue**

The waters of Lake Lyn bubble and swirl, bringing dirt and sand up from the bottom of the lake. There is a slight rumbling sound. Aline Penhallow had never seen anything like it. She was sitting on the sand, but now was standing, looking curiously at the water. The bubbles would pop and dust would puff out of them. Suddenly, the dust all collected in the air and sunk under the surface of the water.

Aline quickly stands and runs to hide behind the closest tree. The water is once again calm, like nothing happened. Abruptly, waves start hammering on the sand, and a head pops up through the white caps. It is hard to tell, but the figure has white hair. Sebastian. A voice booms, speaking the words _Here is your second chance at life. Do not fail. _Aline runs back into Alicante, trying to find someone who will listen to her.

She runs to her mother, Jia, and tells her what she saw. Though she leaves out the voice she heard, thinking that it makes her sound even crazier.

"I don't believe you. That is impossible."

"So, you're going to risk everyones lives, and won't even check into it?!" Aline almost shouts.

"If it will make you feel better, I will send someone out to check."

"It is Sebastian Morgenstern we are talking about, maybe you should send a group."

Jia nods, walking to a phone. She quickly explains what happened, saying just to plainly check and see if it is an exaggeration and dispatches a group of ten shadowhunters to Lake Lyn, much to Aline's relief.

Aline goes to the hill that overlooks the lake. She sees Sebastian surrounded by the shadowhunters Jia sent. They seem to be trying to talk to him, but are all ready to attack with weapons poised at the ready. Sebastian is talking, using a lot of hand gestures. He doesn't seem quite as muscular as he did before. The way he is standing is even different. Less cocky and arrogant, less mean.

Two of the shadowhunters run back toward Aliante. What is going on? Minutes later, Jia and a Silent Brother walk up to Sebastian. The Brother goes to him. He points to his shadowhunters all stand down, putting their weopons away. They tie Sebastian up and walk him back into Alicante. Why are they bringing that monster back into Alicante? He just wants to burn the world down.

Aline runs down and sees her mother. "What is going on? You just brought Sebastian into The Glass City! Do you remember the destruction he caused last time?"

"That is not Sebastian Morgenstern." Jia answers, looking directly ahead of her.

"Yes it is! Everyone knows what he looks like, Mom. You aren't fooling me. If he is here, I am going to stay with the Blackthorns."

"It is not. Brother Enoch is going to run more tests, he is not sure how, but he is quite sure it is, Jonathan Christopher Morgenstern.

~oO0Oo~

Clary was dreading her mothers visit to the institute. She still didn't know about Jace's proposal, and she hadn't had the time to react to the baby growing in Clary's stomach. Jace seemed happy, though. That was what mattered.

When Clary told Jocelyn on the phone that she was pregnant this morning, her mother had gotten very quiet. After a moment, she said that her and Luke would be at the institute around noon. That was at 6, three hours ago. In an hour, Clary knew, she would get the scolding of a lifetime. The only thing was, Clary wanted the baby. She thought about it for awhile and she agreed with Jace, even though it wasn't planned, it was wanted. This little being inside her was wanted. She loved it already.

There was a knock at the bedroom door. Clary opened it to find Isabelle standing there, looking at her.

"Your mom and Luke are downstairs." Isabelle gave a smirk. She knew what was going to be said. She also knew that Clary could handle her mother.

"Okay, lets get this over with." Clary sighed. This wasn't going to be fun.

She walked to the library where she knew Maryse took Jocelyn. When she entered the room everyone looked at her. Jace was already here. He stood and walked to her, slipping his arm around her waist.

"Hi" He whispered.

"Hi" She breathed. How could he affect her like this by saying hi? She felt like she wanted to leave her mother waiting and take Jace to her room.

"So, I'm going to be a grandmother? By my 16 year old daughter? And her 17 year old boyfriend?" Jocelyn was quiet. Clary knew this was bad, when Jocelyn was mad she yelled, when she was irate, she was deathly quiet, but she wasn't about to let her mother put down her family. Jace, the little Bup -her name for the baby-, or her.

"Yes. And you are either going to be apart of its life, or you aren't. Don't ruin it, Mom. If you disapprove so much, you can leave. It may not have been planned, but it's wanted." Clary was just as quiet as Jocelyn.

Maryse's mouth opened slightly in shock at Clary's words, Jace's arm tightened around her. She looked at him to find him looking at her. He was smiling the smile that he saved for her.

"Clary." Jocelyn warned her daughter.

"Mom, I am serious. I am going to be a mom. That is all there is to it. There isnt anything you can do about it. So either suck it up and be a grandmother, or leave. Its simple." Clary was stern. Jocelyn's eyes grew wide. She was shocked that Clary was talking back to her like this.

"I can see you want this." Jocelyn sighed. "I don't like it, but i don't want to ruin my chances either. I still don't approve, but i want to be in your life, and the baby's." Jocelyn visibly relaxed. She knew that she lost the argument, but what was she arguing about? Did she want Clary to abort the baby? Absolutely not! That was her grand-baby!

"Thank you, Mom." Jace felt Clary's muscles loosen in his arms. He didn't realize just how tense she was. He leaned down and kissed the top of her head, then stepped forward to Jocelyn.

"I want to marry Clary, Jocelyn." he said to her. "I was planning to ask, but then I got the news of the baby, and I couldn't wait." Jocelyn's eyes grew wide again.

"Well, I suppose that would be the best option in this situation. Take care of my baby and her baby." Jocelyn gave a small smile to him. She still didn't completely trust him, after everything that happened with Sebastian, but he was dead now, so she was trying to trust Jace more. It was proving difficult.

"It's his baby, too, Mom." Clary said.

"I suppose it is." Jocelyn said.

"well, now that that is finished, Jace, I'd like a word with you." Luke said standing from his chair in the corner. He was so quiet that Clary forgot he was here.

"Yes, sir." Jace said, leading Luke out to the corridor.

"While they are gone, I got a message from Tessa Grey to give to you." Jocelyn pulled out a paper from her pocket and handed it to Clary.

Clary opened it. It read,

_Dear Clarissa, _

_I have some news that I feel that Jonathan should know. I felt that at your mother's wedding he wasn't ready to hear it. He was still discovering who he was. I trust that now he has found himself, with your help. Please give your mother a letter of response as to when you could see me, and Zachariah, too. I do hope we can be friends. _

_With hope at least,_

_Tessa Grey_

Clary's eyes didn't betray her shock at this letter. The conclusion sounded familiar, but Clary wasn't sure where she had heard it before. Why didn't Tessa tell her what she needed in the letter? What could be so important?

"What is it?" Jocelyn asked, curious. She hadn't read it. Good.

"Nothing important." Clary smiled, putting the letter in her pocket.

~oO0Oo~

Jace and Luke walked to the end of the corridor to a large window overlooking the street.

"I'm going to cut to the quick, Jace. Don't hurt Clary. She loves you, its obvious. Don't screw it up." Luke looked directly at Jace. Jace noticed that his eyes weren't normal at the moment, he had the werewolf eyes on display. As a threat.

"I will not harm Clary in anyway, Luke. I love her. I already love that baby that she is carrying. If anything happened to her, I would die a thousand times myself." Jace responded truthfully.

"That had better be true. That is as close to a daughter as I am ever going to have. I intend to take care of her."

"She is my life. Nothing will happen to her if I have any say in it." Jace stated, matter-of-factly.

Luke just nodded then waled back to the library. Jace followed, thinking how happy his life was with Clary. When they entered, Jace noticed Clary slipping something into her pocket. What was that? If it is important, she will tell you, Jace told himself.

"Lets go home." Jocelyn said. Luke nodded and smiled. Both Luke and Jocelyn gave Clary a large hug. They then left the library followed by Maryse. Leaving Isabelle, Jace and Clary.

"Well, that was intense." Isabelle smirked.

"Lets see how your mom reacts to your news." Clary whispered just low enough that Jace couldn't hear. Isabelle frowned.

"Can I talk to you?" She asked.

"Umm, sure." Clary responded. She looked to Jace.

"I'm going to hang out with Isabelle." She smiled.

"Yeah, I want to train out some of the tension from that meeting, anyway." He kissed Clary on the cheek then left.

"Come on." Isabelle grabbed Clary's wrist and led her to her room.

When they entered Isabelle's room, Isabelle locked her door. She then slinked over to the speakers set up in her room. She plugged her phone into it and the song "Casual Sex" by My Darkest Days began to play. Clary noticed that she looped it.

"I don't want to be overheard." She said, explaining.

"What is it, Isabelle?" Clary asked. She was worried about her friend. Her only female friend.

"Ive been thinking, I want to talk to Nicholas Goldscar about Michael Wayland. I also have to return the stele he lent me. I want to ask him questions and maybe a little bit of advice. Is that a bad idea?" Isabelle looked broken. She didn't know who she was. No one else saw it though, she was the same Isabelle, just the facts surrounding her changed.

"Well, if you want to return the stele, use that as the time to ask him about Michael. The worst that could happen is that he refuse to talk to you. And i don't see that happening." Clary responded.

Isabelle smiled, then leaped across the pink fluffy bed spread and hugged Clary. After the shock of Isabelle actually hugging her, Clary just awkwardly patted her back. They were going to have some interesting months ahead.

**How was it? So, I am bringing back Sebastian! Or is it Jonathan? Only I know! I like hearing your ideas, so let me know!**

**PM me and if you want my Kik, let me know, i will give it to you if you want to have a conversation. It doesnt even have to be about my story. I'll chat with ya! Leave a review. They make me want to write and update quicker. The more reviews I get, The more Chapters you get! Its a win-win! **

**Until Next Time...**


	2. Chapter 1

**Hey! So I didn't feel like I gave that much for the prologue, and I was bored, so here is another chapter. Hope ya like it!**

**Chapter 1**

"Well, I want Clary to come with me!" Isabelle whined. She got permission for herself to go to the London institute, but Maryse wouldn't let Clary come, too. She wanted a friend with her. Nicholas was her friend, but she wanted a female friend who was her age. Was that too much to ask?

Isabelle had explained that she made a friend at the Shadowhunter Ball and wanted to visit them. She didn't go into detail, and Maryse was fine with her going, but not Clary. She didn't want to go alone! She knew Jace would give her trouble, but Maryse, too?

"No. Clary is pregnant. Travel through portal may harm the child. I won't be responsible for that."

"Mom, pregnant women travel by portal all the time. The babies are always healthy." Isabelle retorted.

"I will talk to Clary. I will make sure she understands that I feel it could harm the baby. She will then have to ask Jocelyn."

Oh, Jocelyn! She most likely won't let Clary go. Isabelle just nodded. She knew that was as close as she was going to get to a "yes" from Maryse.

Maryse walked away, hopefully in search of Clary. Isabelle sat in a chair in her mothers office. She wanted to talk to Nicholas about her mother. She wanted to return the stele of Michael Wayland's that he lent her. She also wanted to ask him for some advice. Advice on how she should tell her mom what she found out. Advice on how to deal with her Mother when she did tell her. She didn't know how to handle this situation. She also felt that she should tell Nicholas that his best friend had a daughter, and that she wasn't Valentine's daughter. He needed to know. He was probably wondering since Maryse told him she was pregnant.

~oO0Oo~

Clary was sitting on her bed. Jace and Alec were in the training room, so she had some alone time. She was reading the note Tessa gave her. She still hadn't responded. What was so important?

She quickly stood and walked to her dresser. Grabbing a pen and pad of paper, she went back to her bed. She wrote a response to Tessa's letter.

_Tessa,_

_I do believe that Jace has found who he is. He seems more comfortable with himself, though I'm not sure if I had anything to do with it. I would be happy to see you anytime. You and Zachariah could most likely stay at the institute. I would have no problem with seeing you. I enjoyed talking to you at my mother's wedding. I also hope we can be friends._

_Hope to hear from you,_

_Clary Fray_

Now all she had to do was give the letter to Jocelyn. That wouldn't be too hard. Clary didn't want her mother to read it though. She didn't think she would, but you never know. There was a sharp knock at the door. she quickly put all her supplies away and slipped the note to Tessa into her pocket. She was shocked to see Maryse standing at the door.

"Hi" Clary said, her surprise clear on her face.

"May I come in?" Maryse was all business.

"Sure." Clary stepped back, allowing Maryse into the room. They both went and sat on the edge of the bed.

"Isabelle wants to go to the London institute." Clary nodded. "She wants you to go with her. Would you want to go?" Maryse looked like stone. She was all business.

"Well, I'd like to travel. And I'm sure Isabelle would want a friend with her. Yeah, I'd like to go." Clary answered with a smile.

"Well, I am not sure if portal travel would be good on a pregnant woman, might harm the baby." Maryse said like a worried mother, like her mother.

"Women travel by portal all the time when they are pregnant, I'm not worried. I wouldnt go if I was farther along, but I am only about a month into it, I think. I would like to go." Clary said truthfully.

"Alright, if that's what you want. You will have to ask your mother, though." Maryse said.

"Of course." Clary smiled. Maryse got up and walked to the door. She turned again,

"And thank you for making Jace so happy. He isnt my biological son, but i do love him as he is." She walked out the door and was gone.

That was weird. Claary would have to talk to her mom tonight. It was a week since she had told her about the baby. Hopefully she calmed down now. She texted her mom. *I want to come over tonight. Is 5 okay?* within minutes the reply came in. *Yeah. See ya tonight!*

Wow, mom was excited. That was a good sign. Clary stood and looked at the clock. It was 3:30. She wanted something to do. She noticed that Jace had left the copy of A Tale of Two Cities from his father on her nightstand.

She picked it up and opened it, and gasped. So that was why the conflusion to Tessa's letter sounded so familiar. It was written by William Herondale. Did Tessa know him? Is that why she ended her letter like that? Or did she just think of it and use it? There was more to this story than Clary knew.

She began to read. When she made it to the 4th chapter, she looked at the clock. 4:30. Time to go to Mom's. She stood, placing the book back on the nightstand. She wrote a note to Jace letting him know she was going to her mothers.

The walk to Luke's bookstore was slow because Clary was enjoying the spring weather. When she arrived, her mom opened the door. Jocelyn pulled Clary into the house and hugged her. When they walked into the kitchen, Clary remembered Jocelyn throwing a knife at Jace. She remembered Luke getting shot. This house was full of unpleasant memories, along with the memories of her and Simon having sleepovers in the bedroom. Also the more recent memories when she couldn't sleep because she knew Sebastian had her Jace, so Simon had to sleep with her.

Shaking her head she looked at her mom. Jocelyn was smiling at her. This is a big change from a week ago. Why was she so happy?

"I'm glad you came. We've missed you." Jocelyn said.

"I have missed you, too. I was busy, but then Jace found out about the baby and he won't let me do anything. I do lighter training than before and he never takes me hunting anymore." Clary said with a frown.

"He is just trying to protect you and the baby." Jocelyn replied, still smiling. Why was she in such a good mood?

"Could you do me a favor, Mom? Can you get this letter to Tessa? She said that to respond to hers I had to give it to you." Clary handed Jocelyn the letter. Jocelyn nodded, slipping the paper into her jeans pocket.

"I never did get to ask, how did you like the Shadowhunter Ball?" Jocelyn was being really odd, but she seemed happy, so Clary wasn't complaining.

"Yeah. It was a blast. I got to see Simon again, and wear one of Isabelle's beautiful gowns!" Clary grinned at the memory of the golden gown.

For a long time, they just talked. Talked about nothing and everything. But as it started getting later, Clary knew she had to ask if she could go with Isabelle. But she didn't want to upset Jocelyn, especially when she was this happy.

"Mom, Isabelle is going to visit her friend in London. They live in the institute, and she wants me to go with her. You know I've always wanted to travel, and after the baby is here, i won't be able to." Clary almost whined. Might as well tell her everything now.

"Clary, I'm not sure that that is a good idea. What if something happens, I won't be there to help you."

"Mom, I'll be in the Institute there, just like I am in the institute here." Clary explained. "I won't have the chance again, the baby will see to that."

"You do have a point. Will you text me often, and call at least once a day?" Jocelyn was softening.

"Yes. I will send you pictures of the Thames!" Clary exclaimed. "Anything if you'll let me go." "You can go. But you call every day, and text often! If anything strange starts happening, you come straight home! Do you understand my rules?" Jocelyn said.

"Yes! Thank you, Mom! Clary leaped from her chair. She hugged Jocelyn. She had wanted to see London for a long time.

"What's all the commotion?" Luke said, walking into the room.

"Mom said I can go to London!" Clary squealed then hugged Luke.

It was getting late. Clary still had to walk home.

They said their goodbyes, and Clary started on her way home. As she walked past an alley she heard slithering noises. She slowed, reaching into her belt for a seraph blade. She always carried them now. Peering into the dark alley, she could still hear the slimy slithery noises, accompanied by a burning stench. Suddenly a tentacle shot out, grabbed her around the waist and pulled her into the darkness.

~oO0Oo~

Jace was working on agility with Alec. They had decided on one day a week to train together. Today was that day. It was late. Alec went back to his and Magnus's apartment and Jace went to his room to shower. He wondered if he should move Clary into his room? They were engaged to be married, and Clary was pregnant. He would have to ask her.

He got out of the shower and got dressed. Looking for Clary he went to Isabelle's room. They had been spending a lot of time together lately. Isabelle informed him rather rudely that Clary wasn't with her. He slinked to Clary's room, maybe she was asleep already. On the bed was a letter.

_Hey, Jace_

_Went to Mom's. I'll be back later, maybe around 9. _

_Love ya,_

_Clary_

So she went to Jocelyn's? It was already 8:45, so where was she?

Running back to his room, he grabbed his weapons belt and a jacket. He was out of the institute quicker than he had ever fled before.

Seraph blade in hand, he walked down the streets, looking for Clary or any sign as to where she was. She always took the same route to get to Luke's, so she had to be here somewhere.

As he walked, he smelled a burning scent, a demon. Growing more alert by the second, he walked quieter. He began hearing slithering sounds. And a dragging sound. Whatever was being dragged wasn't that heavy. He made it to an alley and the slithering grew louder. He walked into the alley, whispering "Israfiel" to his blade. The seraph blade sparked to life, illuminating the alley.

In this light, Jace saw a nightmare. The demon had six long tentacles, one of which held a small, unconscious red-head upside-down over its discusting, drooling mouth. CLARY!Thousands of teeth were sticking out of the mouth at every angle. The light from the seraph blade shocking the demon, it turned, looking at Jace. It screamed, an ear shattering squeal.

Dropping Clary to the ground, the demon slid closer to Jace. Jace jumped up and stuck the seraph blade into center of the monster. It recoiled, but didn't burn up. The seraph blade was eaten away by the ichor. Pulling another from his belt, Jace screamed "Dumah" and sent the blade flying through the demon's neck, causing the head of the monstrosity to drop to the ground. The body smoked and bubbled, disappearing back to the demon realms.

Jace ran to Clary. She was covered in demon slime. Jace pulled her to him, slid her jacket sleeve up, and drew an iratze on her forearm. He drew another on the back of her hand. He dropped his stele and pulled her to his chest. He cradled her, hoping that she would wake up. He still didn't feel anything. Just a very weak pulse in her neck and heard ragged breathing.

"Please, wake up, Clary. Please, for me." Jace cried into her neck. He couldn't loose her. Looking around him he noticed a seraph blade on the ground. So she did try to fight. But it was just to big for his Clary.

"Mmmm" Clary moaned. That was a good sign. She was still alive enough to feel something. It wasnt good that she was in pain, but she was alive.

"Come on, Clary. You can do it." He slid his hand down to her stomach. "Do it for the baby." Jace said, placing his hand on her belly. Just as his hand met her stomach, she screamed. It was an agonized scream, painful. Jace quickly pulled his hand away. What was wrong?

Lifting her shirt and Jacket slowly, carefully, he saw bruises, and on top of the bruises, cuts smeared with black demon ichor. Small, circular chunks were taken out of the soft skin of her stomach. The tentacles must have had small teeth on them.

An iratze couldn't fix that. He had to get her to the institute, quickly. Pulling her shirt back down, he stood with her in his arms. He made quick time back to the institute. He walked out of the elevator into the corridor. Isabelle was walking out of the kitchen with a sandwich. SHe gasped when she saw them.

"Call Magnus. NOW!" Jace bellowed. Isabelle rushed to get her phone.

Jace put her on a bed in the institutes hospital. He cut her jacket and shirt off. He had to stop the bleeding. There were many cuts, and many chunks taken out of her. He hoped she would be okay.

Isabelle joined him, bringing him gauze, and water. They slowly cleaned the cuts. It was worse than Jace had originally thought. Some of the cuts were deep enough that Jace could see her bones. Hip bones, ribs. They were showing. When they touched the deep cuts, Clary, still unconscious, would scream in agony.

Magnus rushed in. His cat eyes wide.

"Move." He ordered. Isabelle pulled Jace away.

"You have to save them!" Jace yelled.

"Them? There may not be a baby anymore, Jace." Magnus said, pulling off his jacket. "Now, you all have to leave so I can concentrate. If you are here, it will take more time, time Clary may not have."

"I cant leave her!" Jace shouted. Isabelle grabbed his arms and pulled him out of the room. The last thing Jace saw before the door closed was Magnus leaning over Clary.

Out in the corridor, Alec was waiting. He was pale.

"She will be fine, Jace. Magnus knows what he's doing." Alec reassured Jace.

"If she would have told me she was going, I would have gone, too. This wouldn't have happened if I was there. But I wasn't." Jace said, sinking to the floor, his face in his hands.

"You have to stop blaming yourself, Jace. It happened, now we have to be strong for Clary." Isabelle said. She couldn't loose Clary, it would be too much like loosing Max. She was like the sister Isabelle never had.

"I can feel how bad you feel, Jace. You are tormented by this. She will be okay." Alec said, his hand over his parabatai rune.

"Will they both be okay? Clary and the baby, both?" Jace whispered, tears forming in his eyes. He couldn't loose them. Either of them. That was his family. What would he do if Clary didn't come out of that room alive? He would die. He couldn't live without that little red-head. She was his savior. Even when he thought she was his sister, he loved her like no brother should love a sister. When he discovered that he wasn't her brother, he could have done anything, he was so happy. Now he was about to loose her. Her and their baby. The baby he might not ever get to see. The baby that wasn't planned, but was wanted. He might not ever get to toss the child up in the air, might not ever hear the laugh of his unborn child. Might not ever hear Clary's giggle. Never see her concentrate on her drawings again. Never again see how brave she can be when someone threatens her family, threatens him.

He couldn't live without those things. They were what made him who he was. He couldn't live without Clary. Isabelle was pacing, arms crossed across her chest. Alec was watching his parabatai, making sure he was okay. They were quite the group. Waiting for Magnus to tell them that Clary was alive. That the baby was going to be just fine.

Just then, there was another of Clary's screams, filled with pain. Jace winced, Isabelle shuddered, and Alec just closed his eyes, hoping she would be fine, that everyone would be fine.

Magnus walked out to the corridor. He was streaked with blood. Jace's eyes grew wide. Between the blood on the ground where he found her, the blood that covered him and Isabelle, and now the blood on Magnus, he knew she must be dead. No one, shadowhuner or now, can live through that much blood loss.

"She is loosing a lot of blood, too much for her to heal. I need a donor. And only one of you will do. Jace, you and Clary have extra angel blood, come, you can help me by giving blood." Magnus turned on his heel and walked back into the hospital. Jace followed. He sat on the bed next to Clary. She was soaked in blood, now. Her face wasn't peaceful, it was pained. Lines of anguish across her face.

"Jacket off." Magnus ordered, standing in front of Jace with an IV tube. Jace quickly shed his jacket. Almost as soon as the jacket was gone, the IV needle was in his arm. Magnus hooked the tube to a bag.

"I am going to need Alec to put a blood replacement rune on you. It won't work on Clary with all of the demon ichor in her cuts."

Magnus sauntered from the room, returning seconds later with Alec close behind him.

"Since runes applied by a parabatai are stronger, Alec, give Jace a blood replacement rune." Magnus said, walking to a cupboard.

Alec leaned over Jace, and began to draw the rune. Jace never noticed though, he was too busy watching Clary, hoping that his blood would be enough to save her. He would give her all of his blood if it would save her.

"Alec, you have to leave now. The more people who are in here, the longer it will take for her to heal." Magnus said, kissing Alec on the cheek. Alec nodded and left.

"You have to save them, Magnus. Please." Jace said, anguish coloring his voice.

"I am doing what I can. She is bad off." Magnus mumbled, looking down at Clary.

"You know, I knew her since she was a baby. Her mom would bring her for the memory spells. We would sit for awhile, talking, and I would play with little Clarissa, thinking that she was as close to a child as I would ever have." Magnus said, lost in his memories.

"Do you think she will be okay?" Jace asked.

"I hope so, angel boy. She is strong, that is on her side." Magnus said, a smirk trying to form on his lips, but him being too worried to actually smile.

They just sat quietly, as the blood filled the bag. Magnus attatched another tube to the bag.

"You don't have any diseases, do you?" Magnus asked.

"No." Jace answered.

"Good." Magnus stuck the IV into Clary's arm and messed with the switch until the blood was streaming into her arm.

Clary was very pale. She was the color of a sheet of paper. Her jeans were stiff with her blood.

"Okay, Jace. You have to leave now." Magnus said, unhooking him from the IV. "If she needs any more blood, I will come get you again."

Jace nodded and left, looking over his shoulder at Clary.

More waiting. He couldn't hold his tears any longer. Jace sank to the floor again, tears streaming out of the corner of his eyes. He could have saved her if he went with her.

They heard Clary scream again, but this time it was different. This scream had more life to it. All eyes darted to the hospital door. No one came through. Clary was still out. But she was alive, the scream proved it. Jace dropped his head to his knees which he pulled up to his chest, his arms hugging his legs closer. His family. His Clary and their baby. They might die.

Fifteen minutes later, Magnus walked through the door, tears on his face. He looked at Isabelle, then Alec, and finally Jace. Jace could see the sadness in his eyes, and behind that, hope.

"Jace, she wants you." He said with a smile.

Jace sprang to his feet and quickly walked to where his Clary was. As soon as he entered he looked at her. There was more color to her face, now. She still had a look of pain on her face, her eyes closed. Magnus said she was awake, why isn't she awake?

He stood next to her. Her eyes flitted open. Her emerald eyes searching and finding his golden orbs.

"Jace." She whispered.

He smiled at her. "Hey, Clare-bear. How ya feeling?" He had to know how much pain she was dealing with because of him.

"Jace, this isn't your fault. I can see that you think it is, and its not. So stop thinking it is." She whispered. He smirked. She almost died, and she was scolding him. She was going to be fine, she had to be.

"Thats better." She breathed. "The baby?" She asked.

Jace looked to Magnus, who was standing at the end of the bed.

"I won't know until you are better. Sorry, biscuit." Magnus said with a smile.

Clary nodded slightly, then winced. Jace's eyes grew wide, she was in a lot of pain.

"I'm tired. Magnus, can I sleep?" Clary breathed.

"Sure thing, sweetie." Magnus told her. Her eyes darted back to Jace, and he could see all of the pain and sleepiness in them.

"Go to bed, Jace. You need sleep. I'll be fine. Go." She whispered. He smiled at her.

"Yes, Mom." He said, still smiling.

"Go to sleep, Dad." She gave him a very small smile, etched with pain. Jace's eyes grew wide again, but he nodded.

"I'll be here in the morning. Goodnight, Clary." He leaned down and kissed her forehead.

He was back in the corridor. He had to get some rest. Clary would need him in the morning, and she told him to rest, so he was going to.

"How is she?" Isabelle sprang on him.

"She is in pain and tired. She sent me to bed. I am going. Leave her be, she needs rest." Jace answered.

"She told you to go to bed? And you're going? Wow. Jace is actually doing what he's told." Isabelle smarted.

Jace grinned at her. "Goodnight, Izzy. Alec." He treaded up to his room. He changed into pajama pants. He then padded to Clary's room. Pulling the covers back, he sunk into the familiar smell that was Clary. She was going to be okay. They were going to be okay. He was filled with thoughts like this as he finally drifted off to sleep.

**Yayy! That was long! But I was bored. So you get another chapter. School starts next Tuesday, so I'm not sure how quickly the updates will happen. I'm hoping one more before then. So last Tuesday I got to see Kiss and Def Leppard in concert! Def Leppard is my all time favorite, and I cried when the started and when they left. Really hard. Kiss was great, but nowhere near as good as Def Leppard. If you get a chance to see either in concert, take it. They are amazing! Well, anyway.**

**Review! Please! That will insure that I update again before Tuesday! I love ideas, too! **

**Until Next Time...**


	3. Chapter 2

**Hey, another chapter! Is the baby and Clary gonna live? You might find out...**

**Chapter 2**

When Jace woke in the morning with a jolt. The sheets of Clary's bed were wrapped around his ankles. He had dreamed about losing Clary. She was running down the street, smiling over her shoulder at him, giggling. He was following, jogging behind her. She had stopped at the alley, Jace yelled at her to wait, but she just smiled and walked into the alley. Jace ran after her, and just as he got to the alley he saw the Herondale ring he gave Clary on the ground. Looking into the alley he saw her, lying on the ground, looking at him, a large spot of blood on her shirt just over her belly. He ran to her and kneeled next to her. She whispered his name. Then her eyes flickered closed and her chest stopped moving.

He felt so many things at that moment. The most prominent feeling was a longing. The longing for a family with Clary. His family. When Clary told her that she was pregnant he was mad. More than mad. But he went to a Downworld bar to think. And with thinking about something like that, came alcohol. He realized that he wanted a family of his own. He probably wouldn't be a good dad, but he could learn. Clary could help him learn.

Jace got up from the bed, untangling himself from the sheets. He grabbed a shirt he left in Clary's closet and went down to check on her. As he walked closer to the infirmary, he heard moaning. Clary screamed, an ear splitting scream full of anguish. Jace ran to her. Bursting through the door he saw her muscles tighten and relax, her face screwed up in agony.

Jace rushed to her, not knowing what to do. He applied an iratze to her stomach. She seemed to calm, but she still seemed to be in pain. He grabbed his phone and quickly called Magnus.

"Magnus, Clary is screaming with pain. What do I do?" Jace asked, panicky.

"Give her an iratze, that is really all you can do, now. I got her as cleaned up as I could. The demon poison flowing through her veins is reacting with the extra angel blood, making it more painful. So until her body expels the poison, she will be in pain. There is nothing to do."

"There has to be something I can do! She is in so much pain!" Jace almost yelled into the phone.

"There is nothing to do but wait, Jace. Now, after last night, I am going to get some more sleep. Keep an eye on my biscuit." The phone disconnected. Magnus was gone.

Jace looked at Clary to find that her greed eyes were open and looking at him. She was better than she was just a moment ago.

"Jace, I have to pee." Clary whispered. Jace smiled at her.

"Want me to carry you, or do you want the bedpan?"

"I want to use a toilet. Just be careful with my stomach." Clary breathed.

Jace walked to her, and slipping an arm under her knees and behind her shoulders, lifted her. He took her to the bathroom connected to the hospital. Setting her on the toilet, he turned and walked to the door.

"I will wait just outside. I'm not closing the door. Tell me when you're done." With that he walked out to the main room.

A few minutes later, Clary called for him. He lifted her and carefully placed her back in bed. She winced when he pulled his arms away.

"I'm sorry I couldn't protect you." He whispered.

"Jace, stop right there. There was nothing that could be done. Besides, you did save me. I would be lying dead in that alley if you hadn't found me. We might still have the baby, if you hadn't gotten there, we would definitely not have a chance of the baby being alive. So stop blaming yourself." Clary said, her voice weak.

"I can't, you were hurt because I wasn't there. If i'd have been there, we wouldn't be talking about the possibility of our baby being dead, we wouldn't be in the hospital and you wouldn't be in pain."

"We wouldn't be talking at all if you hadn't shown up when you did. And you didn't know that I was leaving, there was nothing you could do. Jace, stop." Clary had a ferocity in her eyes that, last night, Jace wasn't sure he would ever see again.

"I love you, Clary. I was so scared last night. I thought that I'd lost you." Jace said, tears starting to run down his face.

"I love you, too, Jace. I am here, I'm not going anywhere." Clary reached over and grabbed Jace's hand. She hated to see him like this. He was so vulnerable, so much like the 17 year old that he was. She sometimes forgot that they were only 16 and 17 years old. They were going to be parents. It was a scary but welcome thought.

"Do you think the baby is alive, Jace?" Clary whispered.

"I hope so, Clare-bear. I want a family with you." Jace answered.

Clary smiled. How did he make her feel like this? Like she was the only important person in the world.

"I'm tired, Jace."

"Get some sleep. I'm going to shower. I will be back when you wake." Jace smiled. He leaned down and kissed her on the forehead then left.

~oO0Oo~

Clary didn't wake up again that day screaming. She didn't wake up again screaming. Jace was very attentive. If she had to use the bathroom, he carried her in. If she was hungry, he made her some soup. She often thought about the baby, whether it was alive or not.

The next morning Magnus was there when Clary woke.

"Hey. I want to check on the baby. That okay?"

"Yeah. I am dying of curiosity." Clary said.

"Have you had any blood in your panties?"

Clary blushed. "Um, no,"

"That's a good sign." Magnus said.

Magnus placed his hand on her belly. His fingers glowed blue. She felt a tingle in her stomach. Magnus's eyes shined and he smiled.

"Your baby is fine, Biscuit. A little weak, but fine."

Clary smiled. Her eyes lit up like a christmas tree.

"You're sure?"

"Absolutely." Magnus said.

Magnus left and Jace entered. He looked worried. He walked up to Clary. She smiled at him.

"It's alive. A little weak, but alive." Clary's eyes sparkled.

Jace's eyes opened wide and he leaned down and hugged Clary. They were having a baby.

"I called your mom. Told her you were okay. She and Luke were at the lake so she couldn't come, but I told her we had everything under control and you were better."

"Thank you." Clary said.

Clary sat up, she was feeling much better now. The iratze were starting to work now. She stood and walked to the bathroom. When she returned she looked at Jace, hands on her hips.

"I want to go back to sleeping in my room. And I want a shower."

"Alright. Lets go then." Jace smiled.

~oO0Oo~

Clary and Jace went up to Clary's room. Isabelle was waiting to go to London until Clary could go. She had talked to her earlier today about what her mom said. They got the all-clear, but then Clary got attacked. Isabelle didn't want to leave Clary behind. She was the only person who knew that Michael Wayland was her father. She wanted her to go with her.

Simon was supposed to arrive weeks ago, but he changed his mind, giving no reason. Isabelle missed him. She wondered why he didn't show up. He said the Clave needed his help with something, but that he couldn't tell her what. Why? What was so important?

She hoped Clary was okay. The baby, too. She knew Jace and her both wanted it. They just disappeared to Clarys room without saying anything to anyone. Magnus just told her not to worry. But she was.

~oO0Oo~

Jace helped Clary shower. She still needed a little help. He was careful on her stomach where all of the cuts and bruises were.

When they were finished, Clary called her mom. She wanted to reassure her that she was okay. She told her the baby was fine and that she still planned to go with Isabelle to London, it was just delayed.

"I'm happy you and the baby are okay. I was so worried." Jace said as Clary sat next to him on the bed.

"I know you were, Jace. We're fine." Clary smiled at him.

"Lets go to bed. I've missed you." Jace whispered.

Clary nodded and curled up with him and was quickly asleep in Jace's arms.

**So, my sister was going to murder me in my sleep tonight if I didn't update and tell her what happened with Clary. So I did. **

**REVIEW!**

**Until Next Time...**


	4. Chapter 3

**Hey, next chapter. School starts tomorrow, so I don't know when the next update will be. Please Review and the update will happen quicker. I love hearing your ideas, too. Please, give me feedback.**

**Chapter 3**

Two weeks passed and Clary was healed. After the demon poison got out of her system, iratze's began working. She was feeling herself again, and Isabelle was glad. That meant that she could leave and go to London with her, now. Isabelle waited for Clary, and now the wait was over. She was in her room throwing clothes into her duffle bag.

Maryse had been acting weird since Jace announced that he and Clary were having a baby. She was stressing over something that she wouldn't tell anyone else. It had nothing to do with any of them. Isabelle had walked in to find Maryse talking to someone on the phone. She had looked up in surprise when Isabelle entered the room, got quieter and motioned for Isabelle to leave. Something wasn't right.

Jace had catered to Clary all the while she was healing. They were in the training room now. Clary wanted one last training session with Jace before she left. Jace had given quite the stink about Clary going to London without him. But there was nothing he could do, for there was no reason that he needed to tag along. Clary told him that she was going whether he liked it or not, so he had better like it. It was then that he had agreed that she go, because he knew that he wasn't going to win that battle.

There was a knock on Isabelle's door. She walked across the fluffy, pink rug to the door. Clary and Jace were standing there, Jace holding a duffle bag.

"Ready?" Clary asked with a smile. Her red hair was pulled up in a pony-tail.

"Yeah. Let me get my bag." Isabelle grabbed her bag and followed Clary and Jace to the elevator.

They rode down in silence. When they were outside Isabelle saw Alec and Magnus waiting. Alec smiled at her and she went to hug him.

"Take care of yourself, Izzy."

"I will. Just digging for information." She said with a wink.

"Well, be careful of what information you uncover." Alec warned.

"Are we going? I don't have all day." Magnus said loudly. "I'm running out of glitter. I need to buy more."

"Lets go." Isabelle smiled at Clary.

Magnus created the swirling portal. Clary and Isabelle stepped through. They were standing outside the London institute. As they walked through the gate and up the path, Isabelle grew excited to see her friend. She had come to think of Nicholas Goldscar as her friend.

She knocked on the large door. All shadowhunters were permitted in any institute, Isabelle new, but it was always polite to knock. The door opened, and there stood Nicholas Goldscar. He looked shocked to see them, but then smiled.

"Miss. Lightwood. Come, bring your friend." The smile never left his face.

"Hello, Nicholas." Isabelle said with a grin. Clary stood off to the side, not wanting to interrupt the conversation between Isabelle and her friend.

"This is Clary Fray." Isabelle said, gesturing to Clary. Clary smiled.

"Oh, I think everyone knows who you are, Clarissa." Nicholas said, lifting his eyebrows.

Clary chuckled. She usually didn't like being known as Valentine's daughter and Sebastian's sister, but the way Nicholas said it made it funny and bearable.

"Clary, this is Nicholas Goldscar. He knew our parents before the Circle." Isabelle explained.

"I will show you to your rooms. I am glad you are here." He said as he walked, gesturing for the girls to follow. "Everyone else is gone to Idris. The Clave had some immediate threat and wanted reinforcements. Only certain people though. So I am here, all alone." He said, stopping in front of a door. "Isabelle, you can stay in this room, Clary in that room." He said, pointing to rooms side-by-side. The girls nodded.

"Come down to the library when you are ready. I am sure you are here for a reason." He said, slyly.

Isabelle went into her room and began unpacking the important stuff. Toothbrush, hairbrush, that kind of stuff. She grabbed Michael Wayland's stele and walked to Clary's room. Clary was sitting on her bed talking on the phone.

"Yes, I'm safe, Mom. I have to go. Love you." Clary hung up.

"Ready to go down?" Isabelle asked.

"Yeah."

They walked down a flight of stairs to the main corridor where they had entered. One door was open. Assuming it was the library they walked through it, finding Nicholas in a chair by the fireplace, reading a book. He looked relaxed, his long legs crossed in front of him. He looked up at the girls and smiled. Closing his book he gestured for the girls to sit.

They were seated in a small circle. Isabelle handed Nicholas Michael's stele. He took it and looked at it forlornly. Sighing, he placed it and the book on the table between him and Clary.

"So, you have your answer." He said, not questioning, but knowing.

Isabelle nodded. "I want your advice on how to tell my mother and I thought you might like to know, even if you were just slightly curious about the whole thing." Isabelle said, seriously.

Nicholas looked at her steadily for a moment. "So, who is your father? Michael or Valentine?"

"Michael Wayland is my father. I brought Clary because she has helped me through this whole ordeal, and she is a friend."

"Michael Wayland. Wow... That is weird. Your brother's father's parabatai is your father. As you know, he was my good friend, too. So, little Mikey had a daughter! You do have his eyes. I guess Clary could help you through this, we all know she has a father worth that of a squirrel." Nicholas said, looking at Isabelle like family, very familiar.

"Yes. Thank you for bringing up my father again." Clary said with a grin. She would rather not talk about Valentine.

"Well, I do want some advice. How do I tell Mom that I know? I want her to know that I know she went through a whore phase, but I don't know how." Isabelle said with a scowl.

"Well, I'd have to think. When do you plan to return to New York?"

"Tomorrow, late afternoon." Isabelle answered.

"I will have an answer for you. You girls should go sight seeing, though, while your here. There is much to do in the large city. You can visit the Thames. There are pleasant shops. There is Hyde Park. You can feed the ducks. Plenty to do." Nicholas said with a smile. "I will get you an answer to your question before you leave."

"Thank you! So much!" Isabelle squealed. She was happy to be in London, happy to be getting advice from someone who knew her mother so long.

"Well, get going! I will give you my phone number so if you get lost you can call me and i might give you directions back." Nicholas smirked.

Clary's face paled. "Where is the closest bathroom?"

Isabelle's eyes widened.

"Through that door." Nicholas pointed at a door at the far end of the room. His expression betraying his confusion at her sudden request.

Clary darted up from her chair and dashed to the bathroom.

"She is pregnant." Isabelle answered Nicholas's unasked question.

"Ahh. That explains it." Nicholas said.

Minutes later, Clary walked through the door looking weak.

"That was baaaaad." Clary said with a weak smile.

Nicholas laughed. "So, how far along are you? And does your mother know?"

"My mother does know. And my guess is a month, no more than 2 months." Clary said with a smirk.

"Well, would you like to go all touristy with me?" Isabelle asked Clary.

"Yes, lets go all touristy." Clary grinned.

The girls went up and grabbed money and purses. They were going to have a blast. Clary texted her mother letting her know that she was going sight seeing.

~oO0Oo~

There were so many places Clary wanted to see. She wanted to do so many things. As they walked down the street, they stopped at any store that caught there interest. Isabelle bought multiple pairs of black 5 inch heels. Clary bought new converse and more jeans. Her jeans were starting to become more snug, so apparently the baby was already making her body swell. Isabelle bought new dresses while Clary bought Jace a couple of different touristy trinkets. He would like them, just because they were from her.

When they returned to the institute it was late. They looked around for Nicholas, and when they couldn't find him, assumed that he was in bed, so they too, went to bed.

Clary woke later than normal the next morning. She would have still been sleeping if it hadn't been for the bout of nausea that overcame her in her sleep. She rushed to the bathroom and puked into the toilet. She did this so much lately. When would it stop?

She dressed and went to the dining room. Isabelle and Nicholas were already there, eating eggs and bacon.

"Good morning, sunshine!" Nicholas said as she entered.

Clary smiled at him. "Any extra food?"

"We made you a plate." Isabelle said. She slid a plate to the spot next to her. On it was more eggs and bacon. They all talked like old friends.

Later, Clary and Isabelle went shopping and sight-seeing. When they returned, it was 4 in the afternoon. They had bags from multiple shops. Nicholas called them into the library as soon as he heard them enter.

They entered the library after putting their bags in their rooms. Nicholas was in the same chair that he was yesterday. The girls went and sat in the other two chairs.

"Well, I can only think of one way to tell your mother about you knowing about Michael. Just tell her, but nicely. No shouting, sassiness, because I know you are very capable of both. Just tell her that you discovered the truth. NICELY." He emphasized nice.

"That is it!? Just tell her?" Isabelle said.

"That is all you can do. Nicely."

"I wish there was something else I could do."

"Well, I can think of nothing else for you to do." Nicholas said with a smile. "I have summoned a warlock to portal you back. He will be here shortly."

"I could have portaled us back." Clary said.

"Oh, yes. I forgot, you can create new runes." Nicholas looked at her. He was still smiling. His smile was contagious. Clary couldn't help but smile, too.

The warlock showed up at five o-clock. The girls had all of their new belongings in one bag, each. They thanked Nicholas and the warlock and walked through the portal.

Clary walked into the yard of the institute and smiled. Home. Jace. She had missed him yesterday and today. Isabelle was already to the elevator, Clary had to run to catch up. They rode up in silence. As soon as the elevator opened, Jace grabbed Clary and kissed her fiercely. When he pulled away he smiled at her.

"Did you have fun?"

"Yeah. I got you some stuff, too."

"Oh, really?" Jace smiled again.

"Yeah, come on." Clary pulled Jace's arm to her room.

Once they were in she went through her bag. She pulled out a butterfly knife that she thought Jace would like.

"Thanks, Clare-bear." Jace started twirling and flicking it open and shut. Clary loved just watching him.

"Oh, Maryse said that something is going on in Idris. She won't tell me what, but it is big." Jace confided.

"I know. Everyone in the London institute was called to Idris for some big reason no one knows."

Clary pulled Jace to her and kissed him. "Will you shower with me?"

Jace smiled. "Of course."

They spent the rest of the day together.

**So, that was the chapter. Are the characters much like they are when Cassandra Clare writes? I feel like I am straying, let me know please! REVIEW!**

**Until Next Time...**


	5. Chapter 4

**So, next chapter! This one might be more of a transitional chapter. Please review at the end.**

**Chapter 4**

It was 3 weeks since the girls returned from London, and it was obvious that something big was happening. It was killing everyone to know what was going on. Isabelle and Clary more often than ever before. Clary didn't like to be left out for this long. What was so important? Why couldn't they know.

Clary was walking to meet Isabelle by the elevator, they were going to pandemonium with Jace to scout for demons. She met Maryse along the way. She was walking out of the door to one of the empty rooms. She didn't look happy. Clary smiled at her and kept walking.

She made it to the elevator and Jace and Isabelle were already there. Jace grinned at her. He looked stunning, as always, in all black. They were all loaded down by weapons. Isabelle looked impatient. She had been bugging Jace to bring Clary along with them to Pandemonium, but he wouldn't. He finally agreed, but only once until the baby was here. He didn't want to risk another time for Clary to get hurt.

They walked to Pandemonium. Jace was holding Clary to his side as Isabelle walked on the other side of Clary.

"So, what do you think is so important in Idris that has Mom in such a bad mood?" Isabelle asked, stepping over a puddle.

"I have no idea, but I saw her walking out of a spare bedroom and she had quite the scowl on her face. She wasn't happy." Clary added, hugging closer to Jace.

"Well, it probably isn't good, whatever it is. I wouldn't want to be in charge of something bad, it would make me mad, too." Jace said. What he was saying made sense. Why wouldn't something bad have a bad effect on your attitude?

"Well, I want to know what the trouble is." Isabelle complained.

They walked the rest of the way in a companionable silence.

Clary and Jace were waiting outside of the storage room waiting for Isabelle. When they saw her, Clary elbowed Jace in the ribs.

"She's coming."

They followed Isabelle and her suitor into the storage room. Isabelle already had her whip around it, binding its arms to its body.

"Took you two long enough." Isabelle said with a grin.

"We were making out. Hard-core. It was very hot." Jace said, straight faced.

"Can you just kill it, Jace? Or maybe Clary should." Isabelle said with a glance at Clary.

"I will be back, nephilim. Beware." The creature snorted just before Clary stuck a seraph blade in his back. It shriveled up and smoked and vanished.

"Well, that was fun. Want to go hang out with Magnus and Alec for a while?" Isabelle said. She missed her brother.

"Sure." Clary smiled. Jace looked like he was going to protest but decided that he wanted to see his parabatai.

They walked into Magnus's apartment building and went up to his door. Jace knocked and waited. There was a slight sound of feet pounding on the floor. Alec came to the door. He was in pajama pants and a black t-shirt. His eyes grew wider when he saw the group waiting for him. He pulled Isabelle into his arms. When they pulled apart he motioned everyone into the apartment.

They walked in and saw Magnus sitting on the couch in pajama pants and a glittery shirt. His black hair was tussled and sticking every way. He smiled when he saw them.

"Hey, Biscuit!" He jumped up from the sofa.

"Are you guys hungry?"

"Yeah!" Jace said.

"Good, me too. Food!" Magnus went off in search of his phone.

"He's going to order Chinese, you know." Alec said to Jace. "When he orders take out, it is always Chinese."

"Chinese is good." Isabelle said.

Magnus came struting back into the room. "I ordered pizza!"

"You never order pizza." Alec said, surprised.

"Well, I did this time." Magnus said with a wink.

They all ate pizza and talked. They had missed Alec.

"Do you know what is going on in Idris? Maryse is acting all weird and won't tell anyone why." Jace asked Alec.

"No. I have been basically shunned by all shadowhunter. No one but you guys, Mom, Dad, Aline and Helen talk to me, anymore. They talk to me when they feel they have to. That's all." Alec said.

"Well, something is going on. And I don't like it." Isabelle replied shortly.

The walk home was short. No one talked. Jace held Clary close to him. When they got to the institute, Clary decided she wanted a shower after killing those demons. That was dirty work. Jace walked her up to her room. She went about getting her clothes and Jace sat on her bed. She pulled off her shirt and tossed it on the floor. Jace smiled.

"I can already see your baby bump. It is just barely noticeable." Jace said, leaning forward and grabbing Clary around the waist pulling her to him. He bent his head to her belly.

"Hey, little one. You are going to keep me up at night, aren't you?"

Clary gasped slightly. He was really happy about this baby. He said he was, but Clary still wasn't sure.

"I have to get in the shower." Clary breathed.

"I will join you. Did you think that you could strip your shirt off in front of me and not have me all hot and bothered?" Jace winked.

~oO0Oo~

Clary and Jace were laying in Clary's bed when Jace's phone rang. He reached over Clary and answered it.

"Why? It cant be that important. Fine, give us a minute." Jace put the phone down. "Isabelle said Maryse couldn't find us and we have to go down to the library for a meeting."

"Okay." Clary stood and got dressed. Jace just watched her.

"Are you going to get dressed?" Clary asked, smirking.

"No, I was going to go down just like this." Jace grinned. Clary rolled her eyes.

Jace stood and dressed. They walked down to the library, meeting Isabelle along the way.

"So, any idea what this is about?" Jace asked Isabelle.

"Not a clue." Isabelle answered.

They walked to the library and walked in to a shock. Maryse had her back to them and was talking to a boy. The boy was about 18. He was tall, muscular, had a perfectly chiseled face, green eyes and snow white hair. Maryse turned around.

"We have a new occupant of the institute, everyone. This is Jonathan Morgentern."

**Hey. So I left off on a cliffy! Please leave a review. No one is reviewing and the quality of the chapters is failing because I feel that no one is reading this. Let me know what you want to see happen! REVIEW!**

**Until Next Time...**


	6. Chapter 5

**Hey! So my chapters are still sucking, but I am bored, so I shall write. **

**Chapter 5**

Sebastian was standing there, looking at Clary like she was a ghost. What was he doing here? Wasn't he dead? And why did they invite him into the institute?

"Why is he here?" Jace said, looking at Sebastian. He was angry, Clary could tell. His arm tightened around her.

"He will be staying here, Jace. By orders of the Clave." Maryse answered.

"He tried to kill me and Clary, his own sister!" Jace yelled. "I can't let that happen again!"

"That wasn't me." Sebastian spoke up. "That was the demon blood that poisoned my body. The angel Raziel gave me a second chance at the life I, Jonathan, never got because Valentine took it away. He gave it instead to Sebastian."

Jonathan? How could that be?

"How do we know you are telling the truth?" Jace said. "You have lied so many times. Tried to kill me, rape Clary, I cant believe you."

"I understand why you think that that was me. But it wasn't me. That was the demon blood. Remember stabbing me? I was normal for minutes before I couldn't live any longer. Well, the Angel gave me a second chance, a fresh start. Please, give me a chance." Jonathan begged.

"Look at him, Jace." Clary whispered so only Jace could hear her. "He doesn't have that arrogant stance that Sebastian had. He has my mother's eyes. I think he may be telling the truth. I won't trust him immediately, but look at the signs."

He did have the same emerald green eyes that Jace had grown to love. The same eyes that were looking at him through the cover of red hair. He didn't know what to do. If Jonathan was still bad, then he was his family in danger, and Jace couldn't let anything happen to Clary or their baby.

"Just give me a chance." Jonathan pleaded.

"Isabelle, what do you think?" Jace asked.

Isabelle didn't answer. She was staring off into the corner of the room. Clary followed her gaze and gasped. "Simon."

Simon stepped out from the corner. "Hey, Fray." He smirked.

Isabelle stepped forward and ran to him, jumping into his outstretched arms. He swung her around, kissing her. Placing her back on the floor he walked to Clary. Clary hugged him.

"It's good to see you." She breathed.

"You, too." He smiled.

"I am going to show Jonathan to his room. I expect you to all be nice and helpful." Maryse ordered, walking from the room with a sad-looking Jonathan following.

As soon as they were gone, Clary hugged Jace, burying her face in his chest.

"It will all be fine,Clare-bear. I won't let any harm come to you or the baby. You are my family." He whispered into her hair.

"I think he really is my brother, Jace. He seemed so different than the Sebastian who tried to kill everyone."

"I am hungry." Simon declared.

"I think there is some left overs in the fridge. Lets go eat." Isabelle said. She pulled Simon out and Jace and Clary followed them. They went to the table while Isabelle rummaged around the fridge.

"What do you want? Fettuccine Alfredo or pizza?"

"Alfredo." Simon answered, smiling at Isabelle.

"I will warm some up for you two as well." Isabelle said to Jace and Clary.

"Thank you." Clary smiled.

While they were eating they heard footsteps come in the dining room. Clary looked up and stared. Jonathan was standing in the doorway. He looked out of place. She could see that he felt out of place.

"Um, I came down for something to eat. I didn't realize you guys would be here. I can come back if you'd like." He said. Something about the way he sounded shattered something in Clary. He was broken. He didn't know what was going on, either.

"Its fine, Jonathan. There is some more Alfredo in the bowl on the counter, there. You can heat it up and sit down with us." Clary gave him a small, encouraging smile. Wasn't he supposed to be the older brother and look after her, not her looking after him?

When Jonathan was sitting with them, no one said anything. They all just ate. Simon and Isabelle finished their food before anyone else.

"Well, I want to go to bed." Simon yawned.

"Come. I will show you to a room." Isabelle stood. They left the room.

Jonathan just stared at his food. Clary didn't like seeing anyone like this. He looked so lost.

"You don't understand what's happening, either, do you?" Clary finally asked him. He slowly lifted his head to her. His green eyes were filled with sadness.

"No, I don't. All I know is that because of some freak thing that Valentine did, that is no longer in affect, no on e trusts me. I have no one to talk to, and no family to go to. I am utterly alone." He said, almost in tears.

"But you do have a family. I am your sister. I just have to get to know you." Clary said, sliding away from Jace toward Jonathan. Jace watched Jonathan closely, making sure he wouldnt harm Clary.

"But you guys said that you can't trust me. I already blew it once." His face showed all of his sorrow clearly. He was no master at hiding his feelings like anyone raised by Valentine was. Jace still hid his emotions from her, sometimes.

"You will just have to prove your trustworthiness. I believe that you can do it." Clary said.

At that, he started crying. They were the sobs of a broken boy. Clary scooted closer to him and wrapped her arms around him. She held him like she held Jace when he had nightmares. Minutes later he stopped crying, but still held on to Clary. When he lifted his head his face was tear stained.

"Are you done with your food?" Clary asked him. He nodded. She stood, grabbed her plate, along with Jonathan and Jace's and put them in the sink.

"Come on, lets get you to bed." Jonathan stood and let Clary lead him out of the room, Jace following closely behind.

She brought him to his room and opened the door for him.

"Thank you. For wanting to help me. No one else even wants to try to believe me." He said, looking at the floor. Clary's heart went out to him. He was such a broken boy.

"I believe everyone deserves a fresh start. They will come around." She smiled at him.

"Goodnight." He said, closing the door.

It was just Jace and Clary in the hallway. Jace grabbed her hand and pulled her down to her room. They walked in and Jace closed the door.

"I don't trust him." Jace said.

"That is his problem, Jace. No one trusts him, so no one will give him a chance."

"I will give him a chance, but I won't let him be alone with you. If he proves in some very significant way that he isn't Sebastian, then I might think about trusting him, but not before that happens." Jace said.

"Fine. But you will not stop me from helping him. If he asks me for something, I will do my best to fulfill his wishes. I believe that he deserves that."Clary said sternly.

"Okay, but you have to tell me anytime you go somewhere with him. If you are training, I will be there training, too. You won't be alone with him." Jace repeated.

"Fine. Lets go to bed."

"Yeah. It'd been quite the day." Jace agreed.

They climbed into bed and Clary quickly fell asleep in Jace's arms. Jace was too busy thinking to sleep. His thoughts weren't all that pleasant. What if Jonathan did hurt Clary? Clary was his life. Her and the baby that he had yet to meet. He couldn't let anyone hurt them. He loved them too much. He was plagued with these thoughts as he finally drifted off to sleep.

~oO0Oo~

He understood why no one trusted him, he really did. But it hurt. He had a sister, but he didn't know anything about her. He had a mom, but had never met her. He had a whole species who didn't trust him, but had proof that he wasn't who he was. He was changed. The Silent Brothers confirmed that he wasn't Sebastian, but Jonathan. Jonathan was forgotten by all, replaced by Sebastian. And now that Sebastian was gone and Jonathan in his place, no one could let go of Sebastian. It was painful. He wasn't that person.

He was looking at the ceiling thinking that the only person who was nice to him was Clary. She was sympathetic, though, too. He didn't want sympathy. He only wanted a friend. Someone who wasnt afraid of him, to talk to him.

_No, you want someone to hurt. Someone to control. You want a little ginger sex toy. A golden pin cushion. _

Where did these thoughts come from? Jonathan closed his eyes tightly. He didn't want to hurt anyone. He wanted someone to listen to him, but he didn't want control. He wasn;t even going to think about the last two.

When these thoughts ripped through his mind, they hurt. They were unwelcome, and painful. The pain was agonizing when they entered his mind. He didn't know why. He slowly drifted off into a sleep plagued with nightmares.

~oO0Oo~

When Clary woke, Jace wasn't in bed. She heard the shower running. She got up and got dressed. She yelled through the bathroom door telling Jace she was going to get breakfast, then left the room.

Once she got to the dining room she saw Jonathan sitting eating a plate of eggs.

"Hey, there is some extra, if you want some." He said, smiling. The smell of the eggs was making her nauseous. Baby doesn't like eggs.

"Umm, I'm not in the mood for eggs, thanks." She walked to the fridge and grabbed breakfast shake. They were one of the few breakfast foods that didn't make her throw up. She went and sat across from her brother. It was weird, having a brother who was older than you, but that you had never talked to.

Jace walked in, his golden hair still wet from his shower. He was in sweat pants and a black t-shirt. He looked gorgeous. He grabbed a pan and eggs. In one swift movement, he cracked the egg and dropped the insides into the pan. That smell! Clary paled and ran from the room.

"Is she okay?" Jonathan asked, his wide green eyes still looking after Clary.

"Yeah, the eggs have been getting to her lately." Jace responded.

"Odd." Is all Jonathan said, but Jace could tell he was still thinking about it.

"So, are you and Clary serious?" Jonathan asked. He basically knew the answer, but wanted to talk about something.

"Yeah. We are going to get married." Jace said, nonchalant.

"Married? Really? You guys seem young to be thinking about marriage."

"We've been through a lot together." Jace almost snapped. Jonathan was quiet.

Clary walked back in wearing a different shirt.

"I didn't make it." She told Jace who smiled and pulled her to him, kissing her forehead. She went to the fridge and got another breakfast shake.

"Hopefully I can keep this one down." She muttered.

"Are you okay?" Jonathan asked, concern evident in his voice.

"Yeah. I think Jace did that on purpose. He knows what eggs do to me." She said with a playful frown at Jace.

"I didn't do it to make you run, I did it because I wanted eggs." Jace said.

"Why do eggs make you puke?" Jonathan asked, looking between Clary and Jace.

"Should we?" She asked Jace.

"It's up to you." Ke replied, kissing the top of her head.

"Well, the smell of eggs doesn't agree with the baby." She told Jonathan.

"The baby? You're pregnant?!" His eyes were wide. He frantically looked between Jace and Clary. "But, you are only sixteen, right? That is so young."

"It wasn't planned, but it is wanted." Clary told him. "I don't want to hear any negative words on the subject." She stated.

"So, I just met you, and I am already going to be an uncle? Wow..." He left his sentence hanging.

"Would you like to train with us this morning?" Jace asked.

Jonathan's eyes widened. "Yeah, sure."

That morning was a decent morning, they tried to get to know each other. What they didn't know is that Isabelle carried a grudge. Sebastian killed Max. Her baby brother.

**Another semi-cliffy! This was a better chapter than most, but reviews would help. I would like to ask you guys to review. It makes my day. Let me know what I could do better. Let me know what you like, and don't like. I would like to know, maybe I can improve. **

**Until Next Time...**


	7. Chapter 6

**HEYYY! Next chapter. This one is short. Sorry, I have no time with school going.**

**Chapter 6**

It was two weeks ago that Jonathan came to the institute. Clary was 2 1/2 months pregnant and her morning sickness was beginning to subside and her breasts were more sensitive and beginning to swell slightly. She actually looked like she had a chest for once.

Last week, her and Simon went out like they always had. They just walked around and did things they did before they found out about the shadow world. She had missed Simon, and she spent a lot of time with Jace, while Simon spent a lot of time with Izzy. They barely hung out, just the two of them, anymore.

Clary was getting dressed after her shower when there was a knock on her bedroom door.

"Yeah?" Clary yelled. She was fully clothed, just needing to brush through her hair. Isabelle stepped through the door looking hesitant.

"Umm, I just wanted to let you know that I am going to talk to mom about her whoring." Isabelle's voice was laced with disgust.

"I wouldn't use the word 'whoring' when you talk to her if I were you." Clary recommended.

"It depends on how far she pushes me." Isabelle growled. She turned and left. As the door was closing behind her, a hand smacked into the door, pushing it open. Jonathan walked in.

"Hey. Want to train with me? I have realized that I used to rely way to much on the demon blood to fight. I need the training." He asked quietly.

"Um, sure. I'll get Jace." She said. Jace would be mad if he wasn't around Jonathan when he was with Clary.

"Jace doesnt need to be there. If he's busy, there is no need to disturb him."

"Nahh, he likes training with me."

"Okay. Whatever. I'll see you up there." He gave her a shy smile and left.

Clary walked to Jace's room. She walked in to find him sitting on his bed reading a book. It was the copy of 'A Tale of Two Cities' that Stephen had left him. Jace looked up, surprised. He set the book down slowly, looking almost ashamed to be caught reading it.

"What the matter, Clare-bear?" He asked her. He looked worried.

"Nothing. Jonathan wants to train, and I told him I would, but I needed to get you. I knew you wouldn't want me to be alone with him. I would rather not fight about it now." Clary explained.

"You're right, I still don't trust him." Jace said standing. HE walked to her and kissed her.

"Lets go train."

~oO0Oo~

Isabelle walked to her mothers office. As she entered her mother looked at her with surprise. She tried to gesture for her to leave, but Isabelle wouldn't listen. Maryse was going to listen, now.

"We need to talk, Mom." Isabelle said, eyeing Maryse with caution.

"What is it Isabelle, I am very busy."

"I know that Dad isn't really my dad. It is Michael Wayland." Isabelle blurted. She was tired of the secret. Maryse paled.

"What are you talking about, Isabelle?" Maryse said, exasperated.

"I'm telling you that I know the truth. Even went to the Silent Brothers for conformation. It is Michael Wayland." Isabelle said, tensing, waiting for Maryse's response.

"Who have you told?" Maryse whispered.

"Why does it matter who I told?" Isabelle asked, incredulous.

"WHO ELSE KNOWS?" She yelled.

"Clary. Nicholas Goldscar. Alec." Isabelle said, her voice venomous.

"Nicholas." Maryse growled. "He shouldn't have talked to you."

"Why, was there something else you wanted to hide?" Isabelle taunted.

Maryse's face grew red. She was mad. More than mad, irate.

"I didnt want anyone to know. I was hiding it." Maryse whispered.

"Well, I found out. I wish you would have told me." Isabelle breathed.

"I couldnt do that. Only Nicholas knew."

"Why did you do it, Mom? Why cheat on Dad?"

"He made me feel like it was the only choice." Maryse sobbed. "I needed to feel loved. And him cheating didn't make me feel loved."

"That makes sense. As much as I hate to admit." Isabelle said. "I just wanted you to know that I knew." Isabelle breathed. She left the room to Maryse's sobs.

Clary came running downstairs.

"Is everything okay? I heard Maryse yell." Clary said, breathlessly.

"Everything is fine. I just want to be alone for now." Isabelle walked past Clary to her room. She was sick of people lying. Valentine lied to Jace. Jocelyn lied to Clary. Maryse lied to her. It shouldn't happen.

**Hey. Next Chapter was slow. I just wanted to update. I wanted to make Isabelle and Maryse talk. Should Maryse knowing what Isabelle knows make them closer or not? I want a little help on that part. **

**REVIEW!**

**Until Next Time...**


	8. Chapter 7

Hey. Sorry this took so long. Ive been very busy. So please review. It would have pushed me to update. I feel as though the people who are reading dont really like it because i am not getting any feedback. That is all I want, feedback. So here is the chapter!

Chapter 7

A few months had passed and Jonathan had earned trust from everyone, even Jace. That made him feel better about everything. He had friends. He had people whom he could talk to. Jace, Clary, Isabelle and himself were all on their way to Pandemonium. Clary was just a back up, maybe a distraction to mundanes. Now that she was starting to get a baby bump, Jace won't even let her train. It took a lot of persuasion on Clary's part to get Jace to let her come with them today.

Simon was in Idris for a week, then he would be staying at the institute. He was finishing his training. Jonathan didn't know Simon very well. He was in the institute for a week when Jonathan first arrived, then went back to Idris. Everyone in the institute was getting sick of Isabelle running around screaming that Simon was returning.

As they walked into the club, Jonathan noticed how odd mundies were. They like to pretend they know of a world in which they knew nothing about. But that was why it was so easy to slip about around them.

Clary kissed Jace, making Jonathan grunt. That was his sister. His 16 year old sister who was making him an uncle. It was beyond irritating. He should have been able to prevent his sister from this mistake.

Angel boy, too. He just got on Jonathan's nerves. He was all Clary thought about. It was maddening. He had missed out on everything; growing up with a sister, a normal shadowhunter adolescence. He might even have a parabatai, or a girlfriend. But Valentine had different plans. And now that he was here, Clary focused more on Angel Boy than her brother.

Clary left them, walking to the tables and chairs in the corner. Jonathan watched her for a moment, wondering how they looked so different. Where Clary had green eyes and red hair and a slim figure, he had white hair and a very muscular build. How did their looks differ so much?

Jace and Jonathan waited by the storage room for Isabelle. They saw her slink up to the door and a green haired boy follow. The glamor stripped away and they saw what a grotesque demon he really was. Jace opened the door to the storage room and walked in, Jonathan close behind him. They had done this exact routine thousands of times through the last 4 months. So much that they didn't even need to talk to know exactly how to move and kill the demon.

They had the demon slaughtered and left the room. Nothing interesting about that particular kill. Jace immediately went to an obviously pregnant Clary. Usually, at four months, a woman wasn't that obvious, but Clary being so skinny made it very obvious. The mundies could see them now. They had all agreed to just have some fun tonight. Isabelle was already on the dance floor and Jace and Clary were walking out there to join her, Jonathan didn't have anyone That he cared about in any way, and he didn't care for dancing anyway.

He walked to a table and just sat. He watched everyone. They were all so boring, easy to read. There was a couple at a table making out, but it was obvious to Jonathan that the boy only wanted sex, while the girl wasn't willing to give it to him. She tensed when his hand strayed too far, and he would pull his hand back for a moment, then try it again. There was another couple grinding on the dance floor. It was odd to watch. It was like watching people have sex fully clothed.

Just as he was about to asses another couple a man sat across from him. He looked alot like Jace, except his eyes were blue from what Jonathan could tell. The man had runes swirling around his eyes. They were runes Jonathan had never seen before. He could also see that the man had runes peeking out from under his shirt sleeves. He just looked at Jonathan, not saying anything.

Raising his eyebrows, Jonathan said "Do you need something?"

The man just continued to stare. He finally said "You will do quite nicely. Meet me in the alley two blocks down from the institute tonight at midnight." The man stood and walked away. He had a limp and walked slow. What did he want?

Isabelle came and sat in the seat that the strange man had just vacated.

"Who was that? He looked familiar."

"I have no idea who that was. He was looking for his girlfriend. Apparently I looked like the kind of guy who would run off with some guy's gal." Jonathan said. He didn't want anyone to know that that man had wanted to meet. Jonathan wasn't yet sure if he would meet him or not.

"Oh, well then." Isabelle grinned. "You look quite lonely. Come dance." Isabelle stood, extending her hand to Jonathan. "I'm alone, you're alone. We can dance as friends."

Sometimes Isabelle annoyed him. He liked sitting alone. He wasn't much for dancing. He also knew that if he didn't go, Isabelle wouldn't let him be. So he went. He danced with Isabelle. The looks they got were priceless. People would look amazed that two such gorgeous people would be together. Isabelle was beautiful, just not what Jonathan liked. He liked girls with light brown hair, Izzy's was way too dark. She was voluptuous, which he liked, but she was too long and lanky. She also was too girly. Her favorite things to wear were bright pink. That was way to bright for Jonathan to look at. She was fun, though. She knew how to have fun.

~oO0Oo~

Jace was happy Clary talked him into dancing. It had been so long since they acted like the teenagers they were. He loved the little red head in his arms. Her belly was now beginning to grow and she was as gorgeous as ever.

He watched as Isabelle dragged Jonathan to the floor. Everyone had begun to trust him, even Jace. He had helped around here and there. He hadnt done anything that would make anyone think he was like Sebastian. It was weird that he was a different person.

Clary wrapped her arms around his neck, pulling him closer to her.

She shouted to him, "I want some water."

"Come on." Jace led her to the bar. They got waters and went to a table to sit.

"We've been here awhile, I am ready to go home." Clary said, yawning.

"I'll get Isabelle and Jonathan. Then we can go." Jace smiled at her.

He walked passed a group of kids, and pushed his way to Isabelle and Jonathan. They were dancing, and just watching was exhausting. He yelled at Isabelle over the music, "Hey, we are ready to go."

She nodded, "Me too."

Jonathan shook his head, "I am going to stay a little longer. Maybe I'll get lucky." He raised his eyebrows at this last statement. Jace just rolled his eyes.

"Alright, well, we are leaving." Jace and Isabelle walked to Clary.

"Ready? What about Jonathan?" Clary asked.

"He ain't coming." Isabelle said. "Wants to stay and get laid." Isabelle smirked. Clary rolled her eyes. "Well lets go" Jace said.

~oO0Oo~

Jonathan watched as Jace led Clary out of the door and Isabelle following close behind. It was 11:30 now. He had to meet the strange Shadowhunter man in a half hour. He quickly walked out the back entrance, and down the alley toward the institute. It was quite the walk, going around back, but he couldn't let himself get caught.

He entered the alley a block down from the institute and waited. He was a few minutes early. Out of the shadows, a werewolf sprang, claws clamping down on his arms. What was this? The man who came to him in Pandemonium walked up with another man following him. This other man was, from what Jonathan could see in the dark alley, handsome. His jaw was square and he had dark, curling hair. Only when he got closer could he see the burned flesh on his hands, and the same odd runes around his eyes as his blonde counterpart. Who were these men?

"Ahh, Jonathan Morgenstern. Pleased to finally meet you." The dark haired man said. He sneered as he said it. This was a bad idea.

"You look much like your father did at this age. Too bad he can't be here with us." The blonde man growled.

"What do you want? Who are you?" Jonathan asked. How did they know Valentine?

"We want you, young Morgenstern. We want your sister as well, but she always has that golden bodyguard of hers around her. It was easier to get you first." The dark haired man answered.

"You must be careful of how you speak of the young Herondale." The blonde man said, testily.

"I am sorry. But it irritates me. We need them. He is making it difficult." The dark haired man said.

"What do you want me for?" Jonathan spoke up.

"We are seeking revenge on those who killed us and harmed our families. You, your sister, her boy-toy, Isabelle Lightwood and Luke Greymark are all wanted to help us. You see, we have a particular attatchment to Jace Herondale and Isabelle Lightwood, the rest of you were either taken from your families, lied to, or messed with by The Circle. We want revenge on those who destroyed Shadowhunter families for their own gain." The blonde man said. They were both very void of emotion. But it was obvious from the tone of their voices that they werent happy with the circle.

Just then, the werewolf stuck a needle into Jonathan's neck. The fluid that was in the syringe felt cool, rushing into his veins. He felt overcome with the want to do as these men asked.

"Get us Jace Herondale and Isabelle Lightwood. Use these if you must." The blonde man handed two syringes to Jonathan.

"And if you need us," The dark haired man said as they both, with the werewolf, walked to the end of the alley. "Send fire-messages to either Stephen Herondale or Michael Wayland." With that, the men walked around the corner into the darkness.

So, sorry it took so long, I am so much busier than I have ever been. Lot of stuff going on with drama and school and everything. Please review!

Until Next Time...


	9. Chapter 8

sorry. So much happening at once! Please review!

Chapter 8

Jonathan felt the sun on his face. He had gotten home later than everyone else, they were all in bed by the time he got back. He opened his eyes and tried not to think of all that happened last night. Michael Wayland and Stephen Herondale want Isabelle and Jace, and eventually Clary and him. He didn't want to kidnap Jace and Isabelle. That was something Sebastian would do, not Jonathan. And that shot they gave him, made him want to do what they asked for a moment, but was like it wore off now.

Jonathan didn't want to help them. But he had no idea how not to help them. He had a feeling that whatever they had injected him with, would begin to affect him again, he just didn't know when. He sat up quickly.

"I know what to do." He whispered to himself.

He stood and got clothes for the day. He got to the shower, and took a quick shower. He dressed and ran a hand through his white hair. He didn't have time to care if it was dry or not. He walked quickly down the corridor, stopping when he saw a strange woman staring at him with serious grey eyes.

~oO0Oo~

Clary stood in front of the mirror brushing her hair. She needed to get it cut. It was very unruly. Jace was walking around the bedroom, waiting for her response.

"I just feel like we should wait to completely move in together, Jace." She said.

"We are already together all the time. I want to just remove the space completely." Jace said, hopeful that she would just give in.

"Not now, Jace. Maybe as it gets closer to the whole "birthing" thing, I'll think about it. But not now." She said with an air of finality that Jace didn't argue with. "Ok, done. Lets go see whoever is downstairs."

Isabelle had told Clary that a woman was there to see her. She had no idea who. She grabbed Jace's hand and pulled him from the room. As they got near the library she saw two people waiting. There was a skinny boy no older than Jace with black hair. In front of him, stood Tessa Gray.

~oO0Oo~

Jonathan saw the woman with grey eyes was talking to Clary and Jace. Both of their faces showed their shock at whatever she was telling them. He walked to the boy standing behind them. Jonathan recognized him as Brother Zachariah. When did he become human?

"Hi. Can I ask you for some help?" Jonathan said when he got to Zachariah.

"Um, sure. Why don't we go to the library?" Zachariah said with confusion in his eyes.

Jonathan followed Zachariah to the library. The boy knew his way around. He sat in a chair, looking at Jonathan expectantly.

"What do you need? You look distressed, Jonathan."

"Well, I had to tell someone, and you would best know if the Silent Brothers could help me. I was confronted by Michael Wayland and Stephen Herondale."

If the look of astonishment was anything to go by, Jonathan would guess that his chances of the Silent Brothers help just went down.

"They have been dead for years, how did they confront _you?"_ Zachariah asked.

"I was in Pandemonium last night, and Stephen walked up to me. I didn't know who it was at the time. He asked me to meet with him, and I did out of curiosity. He and Michael asked me to kidnap Jace and Isabelle. They then injected something into my neck. It made me want to do what they asked. I don't feel it anymore though. I think it might come back, and I don't want to hurt anyone. Can the Silent Brothers do anything?" Jonathan said. He meant every word he said, he just hoped Zachariah believed him.

"Wow. I believe that the Brothers can help, but they would have to some tests. I am curious as to how they are still alive. They were supposed to be dead for almost 20 years."

"So the Brothers can help?"

"Yes. Will you try to keep me updated?"

"I will try." Jonathan promised.

~oO0Oo~

Clary led Tessa into the dinning room because Jonathan and Zachariah went into the library. Tessa sat across from Jace, while Clary sat next to him. She didn't know what Tessa had to say, but she knew it would affect Jace. If it was negative, she would help him through it.

"Well, why don't I start? My name isn't Tessa Gray. It's Tessa Herondale."

Clary gasped slightly, Jace's eyes widened. "Herondale?" He asked, unbelieving.

"Yes. I am a warlock, and after my husband, William, died, I took my last name back. It caused less problems. Zachariah was Will's parabatai, that is how I know him, too. I know that you have thought that the Herondale family is dead, but it isn't. I am still here. You look so much like Will did. Just you are all light where he was all dark." Tessa's eyes took on a dreamy look. It was obvious that her and Will were happy to Clary.

"I sound much more attractive." Jace muttered. Clary smacked his arm.

"So, you are what my grandma?" Jace asked.

"I would be your great-great-great grandmother. I had gotten married in the late 1870's."

"Wow. That is a long time ago." Clary said. "How can we be sure you are telling the truth. I want to believe you, it is just such a stretch. There has to be some evidence."

"Jace, on your shoulder, do you have a star shaped mark?" Tessa raised her eyebrows.

"How..." Jace was speechless. She knew more than she was letting on.

"Will was the first Herondale to get that mark. It has been on every Herondale after that." Tessa said. "It was from him coming into contact with the Angel Ithuriel."

The door opened and Zachariah peeked his head in. "Am I welcome?"

"Come on in, Jem." Tessa said. He walked in and sat next to Tessa, across from Clary. He gave her a friendly smile.

"Jem? That is Zachariah." Jace said, confused. "Or is there more to this, too?"

"This is Will Herondale's parabatai. His name is James Carstairs." Tessa said.

"I was beginning to want to tell you the truth about who I am. I didn't want to hide anymore." Jem said.

They all just looked at each other. Jace was confused and overwhelemed. Clary was curious. Jem and Tessa looked patient.

"So, how did a shadowhunter come to love a downworder so much?" Jace asked.

"It seems you should know, considering your parabatai is with Magnus Bane." Tessa smiled. She was very friendly.

"You know Magnus?" Clary asked. Of course she does.

"Yes. He helped us when I first moved into the London Institute. But to be more serious about your previous question, I came to the institute seeking refuge, and there I met Will and Jem."

"Oh." Was all Jace said.

"Jem asked me to marry him, and a few hours later, Will. I agreed to marry Jem, but then he became a Silent Brother until a cure to his illness could be found. Will and I remained friends, but it slowly got more serious."

"And I was the cure to Jem's illness." Jace said, connecting the dots.

"Yes. And I thank you." Jem smiled.

"So what are your plans for the future?" Jace asked.

"We will marry in a few months. We shall see where that takes us." Tessa said, smiling at Jem. Her smile was full of affection. He returned her smile, that same look of affection in his eyes.

They all went to the library, just to talk and get to know each other better.

"At Jocelyn's wedding, you played the piano very well." Jem said.

"Thank you. Valentine thought that I should know an instrument."

"I play violin. We should play together sometime." Jem smiled. It was hard to say no to him.

"Yes, that would be amazing. I've actually wanted someone who could play with me, but i never knew anyone who could play an instrument." Jace admitted. He had never told anyone that.

Tessa's phone went off. She looked at the text. Her face clouded. "I have to go to the Labyrinth."

"I will take you. It must be important."

"It was nice talking to you. This is my phone number. If you need anything, don't be afraid to ask." Tessa smiled, handing Jace a piece of paper.

"Goodbye." Jem smiled. They took their leave.

"That was weird." Jace said. "There is still one Herondale left."

"Now maybe you shouldn't act like you are above downworlders. You are part warlock." Clary smiled.

"But I'm better than most shadowhunters. Of course I'm better than downworlders." Jace said.

"Right." Clary said, sarcastically. Just then her phone vibrated. It was Jonathan.

I'm at the Silent City. Please come.

They rushed to the Silent City.

Hey! How was it? I don't think they were in character that well. Please let me know what I can do to make them more in character. I am having issues.


	10. Chapter 9

I am so sorry. I have been super busy! I hope this chapter is good. It is short. Sorry. I will most likely write more when I get home.

Chapter 9

Jonathan was in a cell in the Silent City, waiting for Clary to come. The Silent Brothers weren't comfortable with leaving him out until they could clearly discern the demon substance meant to control Jonathan's will - almost bind him to a demon. He was right back where he started! No one would trust him because some nut had to demonetize him. He had just gotten his family back.

He was lying on the hard cot, looking at the wall. The initials 'JG' were scraped onto the wall. Hopefully Clary didn't think that this was going to completely change him. He would be like, well, like Jace was when he was bound to Sebastian. But there was no mark that he could slash, nothing that anyone could do, because the problem was inside him - once again.

When Clary got here, he decided, he wouldn't let her in the cell with him. What if whoever demonized him decided that that would be a good time to take control? What would happen to Clary? This thought made him completely realize why the Silent Brothers insisted on locking him up. Even he didn't trust himself.

This was going to get a lot worse before it got better.

~oO0Oo~

Clary and Jace rushed into the Silent City and were met by Brother Enoch.

"Where is Jonathan? He told me to come see him here."

He is down in a cell. I believe Jace knows where. I shall bring you to him. Enoch's eerie voice whispered in their minds. Jace's face clouded over for a moment. He remembered those cells. And the screams of the Silent Brothers that Valentine had killed while he was trapped in the cell.

They descended. And descended. Down and down. Further and further. Clary didn't realize just how much there was to the Silent City. She knew that the dungeons were the lowest levels, but this was crazy! They made it to the bottom and Enoch pointed down the corridor. Jonathan is down there.

Clary and Jace passed three empty cells before coming to the one holding Jonathan. He was laying on the small cot staring at the wall. His green eyes shimmered. He turned to them. Giving them a small smile, he sat up and swung his feet around to the floor.

"Hey." He said weakly.

"What's going on, Jonathan?" Clary asked.

"I was confronted by a man at Pandemonium. He told me to meet him, and out of curiosity I did. He and his accomplice met me in an alley. They were Michael Wayland and Stephen Herondale."

Jace's face paled. "What?"

"Exactly what I said. They want me to kidnap Isabelle and you, Jace. And to make sure I do that, they injected me with some kind of demon substance that lets a demon control my will. That is why I am locked in here. So I cannot harm you. I don't want to harm you." Jonathan had his elbows resting on his knees, leaning forward, his arms forward with long fingered hands forming fists.

"Why didn't you take us with you? We could have helped you." Clary whispered.

"I didn't want anything to happen to you. And I'm not sure how much you would have helped. They had two large beasts with them. " Jonathan's eyes had pain etched all through them. "The Silent Brothers took a blood sample and sent it to The Spiral Labyrinth. It is being tested to see what -if anything- can be done. I will remain here until then."

"Are you sure?" Clary asked.

"Clary, he is doing the right thing. He is keeping himself locked away from anyone he might hurt. It's the same thing I tried to do by trying to turn myself in to the Brothers when I was free from Sebastian that one time. He doesn't want to harm anyone, so while he still has a choice, he is locking himself up." Jace told Clary, grabbing her hand.

You must leave now. Enoch's voice said.

"Goodbye, Jonathan. We will do what we can to help." Clary said.

"Yeah. Bye, Jonathan." Jace reiterated.

"Do not put yourselves into any danger. Especially anything that could harm your baby." Jonathan said, sounding as though he were about to cry.

"Don't worry, it will all be fine." Clary shouted as Enoch ushered them out.

Clary and Jace walked back to the institute. It was a slow walk, especially with as cold as it was. Both were lost to their own thoughts.

Clary thought about what she could possibly do to help Jonathan. Talk to Tessa? She would already know because she was part of the Spiral Labyrinth. Could Magnus help? She would have to ask him.

Jace was thinking of ways to protect himself, but more importantly, Clary and the baby. If Clary did something without thinking, like she normally did, what could he do? Even bigger, how could he prevent it?

~oO0Oo~

When Clary and Jace were gone, Jonathan let his feelings flow. Hot tears slid down his face. He hoped that this was enough to prevent harm coming to none he cared about. Isabelle had even begun to grow on him. You know you want to harm them. You want to watch the life drain from Jace's eyes. He has taken what is yours. Clary.

Jonathan scrunched his eyes shut, and covered his ears with his hands. What? He never wants any harm to come to either Jace or Clary. He suspected that this was the remains of Sebastian in his head. He let out a sob; a sob full of pain and anguish. He wished that he had never been sent back. This was just too much. He was a husk of what he should be. He had voices telling him that he wanted to hurt his family. And now he had a demon substance that could control his will. He didn't even want to think of his reign as Sebastian.

This is what broken was. Broken is Jonathan Morgenstern.

Let me know how this one was. PLEASE! I hope you all aren't too mad at me. Who do you think is behind what's happening with Jonathan? I'd love to know what you think. REVIEW! They make my day!


	11. Chapter 10

So, another chapter! Please leave a review afterwords!

Chapter 10

Jonathan sat in his cell. It had been two days since Clary had been here. He was extremely bored. His phone was dead, and even if it wasn't, he didn't get any signal this far underground. He had nothing to do but wait. Wait for an answer as to who he was bound to. And for a way to unbind him.

Jonathan turned and looked out the cell door and started. Brother Enoch was standing there. He opened the cell door.

Come with me.

Jonathan sat up and followed Enoch out to the room. He was led to another room made of stone that was two levels higher than the dungeon. There was a hair in the middle of the room and so many books lined the walls! They were all very old looking books that looked dangerous.

Sit.

Jonathan walked over to the chair and sat down. Enoch grabbed a book off the shelf and opened to a page. He looked at it, with what eyes, Jonathan wasn't sure.

We need another blood sample. Enoch's voice rang into his head.

Jonathan endured all of the pricks and pokes. He wanted this to end, all the suffering. He knew that it could be worse. Clary could still hate him, Jace too. But now they were his best friends. Almost his only friends. The only other friend he had was Isabelle, and she seemed to just tolerate him.

Enoch walked around the room and grabbed random things. He knew what he was doing, and oddly, Jonathan trusted him. Most Shadowhunters didn't seem to really trust being alone with a Silent Brother, but Brother Enoch just had made Jonathan trust him.

The door slowly drifted open and Brother Jeremiah was standing there. He looked at Enoch, then left.

I have something to attend to. I shall take you back to your cell.

Enoch's voice whispered in his mind. Jonathan stood and followed Enoch to the cell. He stepped inside and Enoch locked the door behind him then drifted away, silent as ever.

More time to spend in the dank, dark cell alone. Jonathan was already sick of being locked away down here, but he didn't want to take the chance of harming anyone. He was feeling more and more broken all the time. He just wanted a normal life, a CHANCE at a normal life. He just wasn't going to get a normal life, it seemed.

~oO0Oo~

Clary was pacing her room, waiting for a response. Tessa had given Jace her phone number, and now Clary had just texted her to see if she knew anything that could be done to help Jonathan.

Jace was training, and now that Clary was 5 months pregnant, Jace wouldn't let her train anymore. He was so overprotective. If she trained, it wouldn't harm the little Bup, and she had told him this over and over, and he just wouldn't listen.

Clary wanted to do anything within her power to help her brother. She had come to care for him through these last months. He had changed, her and Jace had agreed. She was happy to have him in her life, if only he could actually be in her life instead of in a cell.

Clutching her stomach, Clary sat on the bed. She was getting bigger. Usually 5 months didn't look that big on women, but since Clary was so small, she looked ready to burst. She still has 4 months to go! If the baby was kicking her like this from the outside she would be black and blue.

The times that she was bored, or was worrying and needed to get her mind off of something, she always daydreamed about how the baby would look. She hoped more than anything that it was a girl. She would love either a boy or a girl, but she just wanted a girl. She dreamed of her baby having Jace's golden, wavy hair, her green eyes, and Jace's confidence.

Her phone buzzed, and looking at it, she saw it was Tessa.

*Jonathan has an odd demon substance in his blood. We will have to analyze it more. I will keep you updated.* Her response didnt really help much.

The door opened and Jace stepped in the door, sweat dripping off from his forehead. He grinned at her, that grin that made the world stop.

"What are you up to?" He asked her.

"I want to find a way to help Jonathan." Clary told him.

"I know you do. There is nothing we can do. The Silent Brothers are already doing what they can."

"I know, but I feel that I should try to help."

"Well, ask Tessa if there is anything she thinks you can do. She is working on the problem, right?" Jace said while he was getting clothes ready for a shower.

"Yeah, I'll ask Tessa."

"Okay. Wanna shower?" Jace said with a wicked gleam in his eye. Clary grinned back at him and followed him into the bathroom.

~oO0Oo~

Isabelle was walking back to the institute after going shopping. She had found a couple of new skirts that she wanted. She was passing an alley when she got a whiff of demon. The stench was obviously something that needed killed. She set her bags down at the entrance to the alley and walked in, taking her whip from her wrist.

As she turned behind a building she was caught by surprise. There were to creatures. They looked like they could have been werewolves, vampires or faeries. Or all in one. Why did they stink like demon?

One of the creatures sprung, and in a nanosecon was on her, knocking her whip from her hand. Her head hit the ground and her world went dark.

Hey! How was it?Please leave a review. I love hearing from you guys. Let me know what you want to se happen. I am always open to ideas!


	12. Chapter 11

Chapter 11

"My daughter has been missing for 3 days, and yet you won't let me search for her?" Maryse yelled at Jia Penhallow, slamming her palm against the desk. Of course, Jia couldn't see her, for she was on the phone.

"You won't be able to look for the specifics of the kidnapping. I have a group of shadowhunters who know what to look for." Jia spoke plainly.

"I should be able to help. That is Amy daughter!"

"What you can do to help is keep Clary and Jace safe. We know that they were after Jace and Isabelle, they could well be after Clary as well."

"I need something to do to aid in finding Isabelle." Maryse choked out.

"I will keep you updated." And with that, Jia was gone, the line was dead.

Maryse cried. She needed her daughter home. Who knew what was happening her? No one knew if she was even alive. No, stop thinking like that, she is okay.

There was a knock on the door. Maryse dried her eyes and took a deep breath.

"Yes?" She called.

Jace walked in. He looked just as worried as Maryse.

"Any news?" He asked.

"None." Maryse shook her head.

"That big oaf they sent to watch us lifted Clary over his shoulder when she went to greet Magnus and pulled her back inside. She was scared at first for the baby, and now I am, so I had to talk to someone who won't make me paranoid."

"We are all going paranoid, Jace. It's being stuck in here like prisoners that's doing it." Maryse sighed.

"Well, we need to do something. And the oaf needs to keep his hand off Clary. I may not be so nice next time." Jace threatened.

"Jace, if you do anything to "the oaf", you could be arrested for going against the Clave."

"So he should save me the trouble by keeping his big paws off my fiancé. Is that too much to ask?" He said.

"I have things that I need to do, Jace. Was there anything important you needed?" Maryse asked.

"No. I just needed some space. I should go check on Clary. Make sure that the oaf is keeping his sweaty mitts off her." Jace stalked from the room, shutting the door behind him.

The Clave decided that with all the times Jace and Clary disregarded them, they had to send a guard to make sure they didn't leave. They must have searched for the biggest meanest person they could possibly find. He was extremely tall, and was highly muscular. He was very ugly. He had a pug face, and a full beard. His looks on top of the fact that he was a fully trained shadowhuner, made him frightfully intimidating.

Maryse sighed. Things were awful. We're they ever going to be able to live a normal life? All of the mischief that the world seemed to want to havoc was happening to them. When were they going to get a break?

~oO0Oo~

Jace was more than mad. The Clave had to babysit him now. And on top of that, the oaf flung Clary onto a couch after man handling her. She was only greeting Magnus. He was sitting across from them in the library now. Clary was curled up against Jace, resting a hand on her slightly bloated belly, on the couch while Magnus had taken a chair.

"I told you, the baby is fine, biscuit. All is well." Magnus spoke to Clary, who was still obviously stressed about their child.

"I know. It just scared me so much. When he slammed me onto his shoulder, it hurt so much." Jace ran his hand down her arm, trying to comfort her. She smiled up at him.

"So how is Alec?" Jace asked Magnus.

"He went to Idris. Didn't he tell you?" Magnus said, looking slightly shocked.

"No, when did her go?"

"He left yesterday." Magnus sighed. "He wants to help search for his sister. This has really gotten to him. He wasn't the same before he left, and I haven't heard from him, which is weird. He always keeps me updated on things while he's away. This is bad, whatever it is."

"Yeah, it is." Jace agreed. But since they were being deliberately kept from any information, he didn't have anything else to say.

An hour later, Magnus took his leave. Clary stood and pulled Jace up from the couch.

"I want a shower." She said, dragging Jace behind her. The oaf followed them to Clary's room, then stood outside the door.

"Why does he have to follow us? We are in my bedroom. How am I going to escape?"

"I escaped from my room once." Jace said, smiling.

"Yeah, well, you're you, so that's different. I'm pregnant, petite and me, I won't be jumping out a window. And I think you've proven that you won't leave my side." She said, smiling back.

They went into the bathroom and showered.

~oO0Oo~

Jonathan sat in his cell. He knew that Isabelle was in trouble. He could feel it. It was his bond. He didn't know what they were doing to her, but he knew it wasn't good. He wished there was something that he could do, but he didn't want to be made into a weapon to be used against his friends.

Then he felt it. It wasn't the first time. His muscles tightened, his hands clenched into fists. He shut his eyes tightly, and felt the pull. It felt like his chest was being pulled. Like there was a string attached to his heart, pulling him to do something unspeakable. The pain was unbearable. All of his muscles were tensed. His fingernails cut into his palms. Then he blacked out from the pain.

~oO0Oo~

Isabelle woke on a hard, cold stone floor. Her head throbbed. She knew she was in trouble. She sat up and saw that she was in a bedroom. It was huge. There was a couch, bed, and a chaise lounge. It was all satin. Red, purple and black. It was beautiful, but sinister. It had an evil hue to it. She didn't like the feeling that it gave her.

She no longer had her whip. Her feet were bare. Then she realized the worst part of it. Where were her clothes? She stood, and walked over to the bed. She noticed there was a chest of drawers on the footboard of the bed. She opened the first drawer. There was panties. All in purple, black or red. All lace. She slipped on a black pair. Then she opened the second drawer, and in it she found bras. Again, all in black, purple or red. All lace. She picked a matching black bra. In the third drawer were nightgowns. Lacy, delicate material. That was all. There were no other clothes to speak of.

She picked a purple nightgown and slipped it over her head. It was the only nightgown that would cover her. The rest were all lace and see-through. It fell just below her bottom, and was extremely low-cut. It was close fitting and showed her curvy figure. The straps hid her bra, but revealed her shoulders.

There wasn't a window or clock in her room, so she didn't know if it was day or night, or how long she had been out. There was a soft creak behind her, making her jump. She turned around and came face to face Asmodeus. He was grinning at her. It was a sickening grin that made her skin crawl and her want to disappear into the floor.

"Hello, Isabelle. Nice to see you again. How do you like your accommodations?" He said to her.

"What am I doing here? Why do you want me?" She asked.

Asmodeus sighed. "I am going to have to teach you some manners. You must be polite and answer first the question given you." He growled.

"I prefer my own room, in the institute, thank you." She said with contempt.

"That wasn't very polite." He told her.

He sprang on her, knocking her onto the bed. Before she knew what happened he had one of her wrists manacled into a cuff attached to the bed. She kicked and screamed, thrashed and bit, but he took pleasure in her attempts to free herself.

Soon he tired of her trying to fend him off, he slammed his fist into the side of her head, which stopped her moving long enough to get her other hand into the cuff. He slowly worked his way down to her feet. She moaned, just beginning to regain consciousness. He felt his member jump. He had waited three days for her to wake. And now she had.

Hey. Happy Thanksgiving! I feel as though I should bump up the rating on this now...

I wanted to go more into detail on what was happening here, but I thought I should ask. So, for future reference, more detail, or leave it like this? Please let me know, because I don't want. anyone to get scared off when they really like the story. REVIEW!


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